BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013321.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,715,170 number of mapped reads = 1,356,737 (79.1%) number of supplementary alignments = 14,827 (0.86%) number of secondary alignments = 0 number of mapped bases = 87,613,934 bp number of sequenced bases = 87,576,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,572 duplication rate = 8.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7366 >>>>>>> ACTG content number of A's = 23,516,812 bp (26.85%) number of C's = 16,510,306 bp (18.85%) number of T's = 27,376,037 bp (31.26%) number of G's = 20,162,186 bp (23.02%) number of N's = 10,793 bp (0.01%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 681,460 number of insertions = 6,026 mapped reads with insertion percentage = 0.44% number of deletions = 21,972 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.3094X There is a 1.77% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6187449 0.024824206957542547 0.47818133701681026 chr2 243199373 6815909 0.028026013866409103 0.4009174453886585 chr3 198022430 6246168 0.031542729780661714 0.26766609783466006 chr4 191154276 5757840 0.030121429248069764 0.2616263639286692 chr5 180915260 6516563 0.036019974213341646 0.2867592551048809 chr6 171115067 5551699 0.032444244082842806 0.30108909626446845 chr7 159138663 4280872 0.026900263702730742 0.3069978204002429 chr8 146364022 5171900 0.035335869630584486 0.3459714232276868 chr9 141213431 3265592 0.023125222415989594 0.2592741563729092 chr10 135534747 4302914 0.03174768164801311 0.30971984806769787 chr11 135006516 3080757 0.022819320809671143 0.24564945906895386 chr12 133851895 3167475 0.023664028066244413 0.23367860102616717 chr13 115169878 2892130 0.025111861280255936 0.24054516348822033 chr14 107349540 3020255 0.028134773563072556 0.25801962050420696 chr15 102531392 2823484 0.027537751560029536 0.24860560912820726 chr16 90354753 2618284 0.028977822561254748 0.2631799311045845 chr17 81195210 2554487 0.03146105539969661 0.2769940138255785 chr18 78077248 2870911 0.036770135648223665 0.3743862783956852 chr19 59128983 1916059 0.03240473457830317 0.3817764099506507 chr20 63025520 1709871 0.0271298197936328 0.25337244056888697 chr21 48129895 1155373 0.024005308966495772 0.23364361315917373 chr22 51304566 872957 0.017015191201500468 0.1949834069230182 chrMT 16571 42729 2.5785408243316637 3.0624324595117467 chrX 155270560 4580779 0.029501915881542516 0.26019126610629534 chrY 59373566 211477 0.003561803917925361 0.0948927054452597